GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pseudomonas fluorescens GW456-L13

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate PfGW456L13_5091 Triosephosphate isomerase (EC 5.3.1.1)

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091
          Length = 247

 Score =  231 bits (589), Expect = 1e-65
 Identities = 123/246 (50%), Positives = 163/246 (66%), Gaps = 2/246 (0%)

Query: 5   LVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQ 64
           +V GNWK++G+R  V EL++ LR +LA  +   VA+ PP ++I+      EG  I +GAQ
Sbjct: 1   MVAGNWKMHGTRASVAELINGLR-DLALPSSVDVAVFPPFLHINQVIEGLEGKSISVGAQ 59

Query: 65  NVDLNLS-GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123
           N  +    GA TGE + + L D G   +++GHSERR    E D ++ +KFA  +  GLTP
Sbjct: 60  NSAVESGQGALTGEVAPSQLVDAGCSLVLVGHSERRQILGEQDAVLIRKFAAAQACGLTP 119

Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQA 183
           VLCIGET  + EAGKT EV +RQ+ ++++  G  AF  AVIAYEPVWAIGTG +ATP QA
Sbjct: 120 VLCIGETLEQREAGKTLEVVSRQLGSIIEELGVGAFAKAVIAYEPVWAIGTGLTATPQQA 179

Query: 184 QAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFA 243
           Q VH  IR  +A  ++ +A+ V + YGGSV A+NA ELF  PDIDG L+GGASL AD F 
Sbjct: 180 QDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFGMPDIDGGLIGGASLNADEFG 239

Query: 244 VIVKAA 249
            I +AA
Sbjct: 240 AICRAA 245


Lambda     K      H
   0.316    0.130    0.366 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 187
Number of extensions: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 247
Length adjustment: 24
Effective length of query: 231
Effective length of database: 223
Effective search space:    51513
Effective search space used:    51513
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate PfGW456L13_5091 (Triosephosphate isomerase (EC 5.3.1.1))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00419.hmm
# target sequence database:        /tmp/gapView.12867.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00419  [M=228]
Accession:   TIGR00419
Description: tim: triose-phosphate isomerase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                               Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    1.5e-67  213.7   1.4    1.7e-67  213.5   1.4    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091  Triosephosphate isomerase (EC 5.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091  Triosephosphate isomerase (EC 5.3.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.5   1.4   1.7e-67   1.7e-67       1     228 []       1     236 [.       1     236 [. 0.95

  Alignments for each domain:
  == domain 1  score: 213.5 bits;  conditional E-value: 1.7e-67
                                               TIGR00419   1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.sei 54 
                                                             +v +n+K+++++ +v+++++ l+ ++a ++ v vav ppf++++ v + +e   i
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091   1 MVAGNWKMHGTRASVAELINGLR-DLALPSSVDVAVFPPFLHINQVIEGLEgKSI 54 
                                                             699******************97.79*************************999* PP

                                               TIGR00419  55 qvaAqnvdav.ksGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkv 108
                                                             +v+Aqn  +   +Ga tGe+    l+d+G+  vl+gHsErR +l e d ++  k+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091  55 SVGAQNSAVEsGQGALTGEVAPSQLVDAGCSLVLVGHSERRQILGEQDAVLIRKF 109
                                                             ******9986257****************************************** PP

                                               TIGR00419 109 arlkelglksvvCvgetleereaartinnvattaaaaA.......lepdvvAvEP 156
                                                             a +++ gl++v+C+getle+rea++t+++v ++ + +        + ++v+A+EP
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091 110 AAAQACGLTPVLCIGETLEQREAGKTLEVVSRQLGSIIeelgvgaFAKAVIAYEP 164
                                                             **********************99999999888877766666666********** PP

                                               TIGR00419 157 veliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211
                                                             v++iGtG ++++ +a+ v++ +r  l+  + eva+ vr+lyG+sv+aa+++el+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091 165 VWAIGTGLTATPQQAQDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFG 219
                                                             ******************************************************* PP

                                               TIGR00419 212 qldvdGvLlasavlkae 228
                                                              +d+dG L+++a+l a+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5091 220 MPDIDGGLIGGASLNAD 236
                                                             **************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (228 nodes)
Target sequences:                          1  (247 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.62
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory